[gmx-users] pdb2gmx eats a bond
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 22 18:28:48 CEST 2010
Thomas Schlesier wrote:
> Hi all,
> i have built an .rtp entry for a molecule with 310 bonds, for the opls
> force field. For pdb2gmx i use the following command (version 4.0.7)
> *pdb2gmx -f CAT.pdb -o -p -ignh -ter*
> -ter is there because it is no protein, and use no C- and N-terminus
> (since there are none).
> Her one question, the option -ter works (i think) but it is not listed with
> pdb2gmx -h
> Are there any reasons.
The -ter option is listed for me in 4.0.7:
-[no]inter bool no Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool no Interactive termini selection, iso charged
-[no]lys bool no Interactive Lysine selection, iso charged
The option certainly works, if that's the concern.
> The relevant output line of pdb2gmx is then
> *Number of bonds was 310, now 309*
> -> So pdb2gmx ate a bond.
> Has anybody an idea why this happens?
I don't know all of the underlying code, but I frequently see a bond removed
from most of my protein structures.
> Has anybody an idea which could be the fastest way to find out which
> bond is missing?
Run a short MD and see if any of your atoms drift away :)
> Are the [ angles ] and [ dihedrals ] section also affected by this
> (since if i understood it correctly pdb2gmx uses the [ bonds ] section
> to determine the other two sections)?
Potentially, but until you test to see if any bonds are actually missing,
there's nothing to diagnose in these sections.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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